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Change to test TSAN with clang and libomp
2018-10-05
Mark Abraham
Change to test TSAN with clang and libomp
commit
|
commitdiff
|
tree
2018-10-05
Roland Sch
u
lz
O
CL: Mak
e
variab
l
es const
commit
|
commitdiff
|
tree
2018-10-05
M
.
E
ric Irrgang
A
d
d gmxapi::System
.
commit
|
commitdiff
|
tree
2018-10-05
S
z
ilárd Pál
l
Update test matrices with new
G
P
U specifiers
commit
|
commitdiff
|
tree
2018-10-04
B
erk Hess
Ma
k
e
A
VX2 p
a
ss
TSAN
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Ex
t
ract helper
f
unctions for prepa
r
ing f
o
r appending
commit
|
commitdiff
|
tree
2018-10-04
M
ark Abraham
Simplify EM usage of mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
U
se fast r
e
turns i
n
md5 com
p
utation
commit
|
commitdiff
|
tree
2018-10-03
Mag
n
us Lundb
o
rg
Allow using COM of
previous st
e
p as P
B
C
r
efe
r
enc
e
commit
|
commitdiff
|
tree
2018-10-03
M
a
rk Abraham
Add e
n
d-to-end te
s
ts of energy
m
inimiz
a
tion
commit
|
commitdiff
|
tree
2018-10-03
Paul Bauer
Disable GMXAPI w
h
en o
n
ly bu
i
lding mdrun
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric I
r
rgang
Add gmxapi
:
:Contex
t
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
Move mdrun mainFuncti
o
n
t
o clien
t
c
od
e
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrg
a
n
g
Ad
d
test data fo
r
gm
x
api
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
r
ic
I
rrg
a
n
g
Add gmxapi exceptions
.
commit
|
commitdiff
|
tree
2018-10-02
Paul Bauer
Fix
include
form
a
tti
n
g in gmxapi
commit
|
commitdiff
|
tree
2018-10-02
Roland Schulz
Use subgroup shuffle for
reduct
i
o
n
commit
|
commitdiff
|
tree
2018-10-02
Be
r
k
H
e
ss
Update DD cutoffs for
up
d
ate gr
o
ups
commit
|
commitdiff
|
tree
2018-10-02
Mark Abraham
Red
u
ce md
r
u
n
tests u
s
ing group scheme
commit
|
commitdiff
|
tree
2018-10-01
Mar
k
Abraham
Fix
g
c
c-8 warn
i
ngs about str
i
ng
s
commit
|
commitdiff
|
tree
2018-10-01
Paul Bauer
Change get
_
a
tom
_
inde
x
to retur
n
int
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
Ad
d
rele
a
s
e
not
e
s for
r
emoving non-reproducibl
e
aspects
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraha
m
Tests for m
d
5
computation
o
n
open files
commit
|
commitdiff
|
tree
2018-09-29
Mark Abrah
a
m
Stop
ICC
I
C
E
commit
|
commitdiff
|
tree
2018-09-29
Berk Hess
Add UpdateGroupsCog
t
o
DD
commit
|
commitdiff
|
tree
2018-09-28
M
a
rk Abraham
Use more
d
efault ini
t
ialization of mdrun structs
commit
|
commitdiff
|
tree
2018-09-28
Mark Abr
a
ham
Make some sym
b
ols in gmxpre-co
n
fig
.
h always defined
commit
|
commitdiff
|
tree
2018-09-27
Kevin Boyd
Reduce preprocessor de
p
end
e
ncy in reso
u
rcedivi
s
ion
.
cpp
commit
|
commitdiff
|
tree
2018-09-26
Berk
Hess
Ex
t
ra
c
t sett
l
e test w
a
te
r
co
o
rdinates
commit
|
commitdiff
|
tree
2018-09-26
Magn
u
s Lundborg
Added pullChe
c
kPbc
W
ithinGroup() to c
h
eck one
g
roup
commit
|
commitdiff
|
tree
2018-09-26
Mark Abraham
C
larify dis
t
inct paths for mdrun log file handling
commit
|
commitdiff
|
tree
2018-09-25
Berk Hess
Add UpdateGroupsCog clas
s
commit
|
commitdiff
|
tree
2018-09-25
Pasc
a
l Merz
R
e
mov
e
obsolete braces in do
_
md
(
)
commit
|
commitdiff
|
tree
2018-09-25
Pasc
a
l Merz
R
emove rerun from
d
o
_
md
commit
|
commitdiff
|
tree
2018-09-24
M
.
Eric Irrgang
F
i
x
gmxapi::Version test regression
.
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fi
x
p
e
rfo
r
mance
re
p
ort when init_
s
tep
!
=
0
commit
|
commitdiff
|
tree
2018-09-24
Mark Abraham
Fix Doxygen links
commit
|
commitdiff
|
tree
2018-09-23
Mar
k
Abrah
a
m
Leak les
s
from gromppp
w
ith
cmap
commit
|
commitdiff
|
tree
2018-09-22
B
erk Hess
Add
u
pdate
g
roups boolea
n
t
o
DD
commit
|
commitdiff
|
tree
2018-09-22
Be
r
k
H
e
s
s
Rename DD cons
t
r
a
int boolean
s
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Add update
groups
commit
|
commitdiff
|
tree
2018-09-21
Szi
l
árd Páll
Bump tes
t
timeout only for OpenCL integ
r
a
tion tests
commit
|
commitdiff
|
tree
2018-09-21
Roland S
c
hulz
Fix clang-tid
y
w
a
r
nings for clan
g
7
commit
|
commitdiff
|
tree
2018-09-20
M
ark
Abrah
a
m
U
p
date to test wit
h
c
l
ang-7
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Change p
u
ll bu
f
fers to s
t
d::vector
commit
|
commitdiff
|
tree
2018-09-18
Be
r
k He
s
s
Introduce
e
xtractILists he
l
per function
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraham
Separated
p
a
rtiti
o
ning and dlb co
d
e
w
ithin domdec
commit
|
commitdiff
|
tree
2018-09-18
Pasc
a
l Merz
I
n
troduc
e
stop
h
and
l
er
commit
|
commitdiff
|
tree
2018-09-18
Pasc
a
l Merz
Introduce
checkpoint handler
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Introduc
e
rese
t
han
d
le
r
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraham
Add not_null fro
m
GSL
commit
|
commitdiff
|
tree
2018-09-18
Rola
n
d Schulz
Fix bitmask printi
n
g
commit
|
commitdiff
|
tree
2018-09-17
M
.
E
r
i
c I
r
rgang
Fra
m
ework in which
t
o
b
uild
g
mxapi
.
commit
|
commitdiff
|
tree
2018-09-17
Paul
B
auer
Properly ini
t
i
a
l
ize idef in topolog
i
e
s
commit
|
commitdiff
|
tree
2018-09-17
B
e
r
k Hess
Move
i
func
s
tuff from id
e
f
.
h to if
u
nc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Kevin B
o
yd
Added basic
t
e
sts
for gmx
msd
commit
|
commitdiff
|
tree
2018-09-16
Joe Jorda
n
Move variabl
e
s
aroun
d
in
pdb2gmx
commit
|
commitdiff
|
tree
2018-09-14
M
.
E
ric
I
rr
g
ang
Rearrange mdr
u
n/runner
.
h
commit
|
commitdiff
|
tree
2018-09-14
Paul Bau
e
r
In
t
roduce g
m
x
rep
o
rt-m
e
t
ho
d
s
commit
|
commitdiff
|
tree
2018-09-13
Be
r
k H
e
s
s
Add C
+
+ version of t_ilist
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Con
v
ert v
s
ite stru
c
t
s
to C+
+
commit
|
commitdiff
|
tree
2018-09-12
M
.
Er
i
c Irrgang
Si
m
pl
i
fy add_su
f
fix_
t
o_
o
utput_na
m
es()
commit
|
commitdiff
|
tree
2018-09-12
Roland
S
c
h
ulz
R
emove
c
pluscplus i
f
de
f
s
commit
|
commitdiff
|
tree
2018-09-12
Ro
l
and Schulz
Fix cla
n
g-tidy
war
n
ing
s
for OCL
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Co
n
vert
D
D gm
x
_re
v
erse_
t
op_t
t
o C++
commit
|
commitdiff
|
tree
2018-09-11
Mark Abrah
a
m
Replace C-
s
tyle library fi
l
e handling with RAII
ap
p
roaches
commit
|
commitdiff
|
tree
2018-09-11
Mark Abraha
m
Improve
D
D logging
commit
|
commitdiff
|
tree
2018-09-11
Roland
Sch
u
lz
Com
p
ile
n
onbonded kern
e
ls
a
s C++
commit
|
commitdiff
|
tree
2018-09-11
David van der Sp
o
el
A
d
ded option to gm
x
nmeig to print ZPE
.
commit
|
commitdiff
|
tree
2018-09-11
Mark Abraham
R
eplace readConforma
t
i
o
n wit
h
Topo
l
ogyInformation
commit
|
commitdiff
|
tree
2018-09-11
P
ascal
M
erz
Added trivial const
q
ualif
i
ers
commit
|
commitdiff
|
tree
2018-09-11
P
a
s
cal
Merz
Initia
l
ize total_v
i
r and pres in init_md
commit
|
commitdiff
|
tree
2018-09-10
R
oland Schul
z
Replace roundi
n
g using
int(x+0
.
5) wi
t
h
roundToInt
commit
|
commitdiff
|
tree
2018-09-10
Roland Schu
l
z
A
dd roundToInt
commit
|
commitdiff
|
tree
2018-09-09
M
ark Abraham
Change TopologyInformation
i
mplementation
commit
|
commitdiff
|
tree
2018-09-09
Paul Bauer
Remove macro for group type in topology
commit
|
commitdiff
|
tree
2018-09-07
M
ark A
b
raham
Fi
x
grompp me
m
or
y
leaks
commit
|
commitdiff
|
tree
2018-09-07
Roland Sch
u
lz
c
l
an
g
-tidy: ov
e
rride
commit
|
commitdiff
|
tree
2018-09-07
Magnus
Lundborg
C
heck q
perturbation when PME on GPU is tested
commit
|
commitdiff
|
tree
2018-09-06
Roland Schulz
H
os
t
Allocator: Re
m
ove unnecessa
r
y template
commit
|
commitdiff
|
tree
2018-09-06
R
ola
n
d
Schu
l
z
Remove
p
in/unpin f
r
om
Host
A
llocat
o
r
commit
|
commitdiff
|
tree
2018-09-05
Paul Bauer
Change
s
to docume
n
tati
o
n build scrip
t
commit
|
commitdiff
|
tree
2018-08-30
P
a
ul Bauer
More fixes from
c
lang-tidy-7
commit
|
commitdiff
|
tree
2018-08-30
Christia
n
Blau
St
o
re es
s
ential dynamics param
e
ters
as vec
t
ors
in
s
tead
.
.
.
commit
|
commitdiff
|
tree
2018-08-30
Mark Abraham
Upd
a
t
e
tes
t
in
g
mat
r
ices f
o
r
co
v
erage and speed
commit
|
commitdiff
|
tree
2018-08-29
Mark
Abraham
Merge
bra
n
ch
release
-
2
018
commit
|
commitdiff
|
tree
2018-08-29
Berk He
s
s
Refactor wall potenti
a
l
calcul
a
t
ion
commit
|
commitdiff
|
tree
2018-08-29
Rola
n
d Schulz
Use more const in hardwaretopology
commit
|
commitdiff
|
tree
2018-08-29
Roland Sch
u
lz
Fix clang-tidy buil
d
with libstdc
+
+
>
=
7
commit
|
commitdiff
|
tree
2018-08-29
M
a
rk Abraham
Move
c
lang
-
tidy build
commit
|
commitdiff
|
tree
2018-08-28
Mark Abra
h
am
F
i
x more clang-tidy is
s
ues
commit
|
commitdiff
|
tree
2018-08-28
S
zilárd Páll
Qu
i
et cmake abo
u
t clFFT
not fou
n
d after fir
s
t run
commit
|
commitdiff
|
tree
2018-08-28
bori
s
tim
Updates to gmx cluster
commit
|
commitdiff
|
tree
2018-08-28
R
o
land Schulz
Add hard limit fo
r
li
n
e length
commit
|
commitdiff
|
tree
2018-08-27
Mark Abraham
Fix use of nullp
t
r
commit
|
commitdiff
|
tree
2018-08-27
Paul Bauer
T
ra
n
sfer information from old how
-
to section
commit
|
commitdiff
|
tree
2018-08-27
Rola
n
d Schulz
Ena
b
le
mo
r
e
c
lang-tidy checks for new code
commit
|
commitdiff
|
tree
2018-08-24
Mark Abraham
Fix buil
d
wi
t
hout TNG
commit
|
commitdiff
|
tree
2018-08-24
Ma
r
k
Abra
h
am
Merg
e
branch release-2018
commit
|
commitdiff
|
tree
2018-08-22
Paul Bauer
Fix trjconv when
ru
n
n
i
ng without a stru
c
ture file
commit
|
commitdiff
|
tree
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